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scvi-tools · k-dense-ai — Claude Code skill: what it does, how to install

Guides probabilistic modelling for single-cell omics data. Use it for batch integration, cell annotation, multimodal data, and model-based uncertainty.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill scvi-tools -a claude-code
Open on GitHub

What scvi-tools does

This skill guides work with scvi-tools across RNA, ATAC, CITE-seq, methylation, cytometry, and RNA velocity. It matches a task to a model: SCVI for RNA integration, SCANVI for annotation with partial labels, TOTALVI for RNA plus protein counts, and MULTIVI for RNA with ATAC. It also covers posterior differential expression and reference mapping.

For an RNA workflow, the skill checks cell and feature identifiers, non-negative integer counts, and batch metadata. It then lays out QC, feature selection, registration through setup_anndata or setup_mudata, model training, and checks of validation history, seed stability, and retained biology. Use scanpy for standard preprocessing and exploratory work.

Python 3.12+ and scvi-tools with dependencies for the chosen model are required. Do not reconstruct counts by exponentiating log-normalized values; that is a reason to inspect matrix provenance before model registration. CPU is supported, while accelerator needs depend on PyTorch and the hardware.

What it helps with

  • integrate RNA data across batches
  • annotate cells from partial labels
  • combine RNA and ATAC in MuData
  • model CITE-seq RNA and protein counts
  • validate count matrices before training

Example prompts for the agent

  • "Choose a scvi-tools model for RNA batch integration and prepare the `AnnData` object."
  • "Check `rna_counts.h5ad` before `SCVI.setup_anndata` and preserve the count layer."
  • "Show how to train `MULTIVI` on registered `MuData` containing RNA and ATAC."

How to install scvi-tools

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill scvi-tools -a claude-code

2Manually: put the files in place

~/.claude/skills/scvi-tools/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/scvi-tools/

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Other versions of scvi-tools

scvi-tools official anthropics A skill providing deep learning workflows for single-cell genomics with scvi-tools. It guides model selection, batch correction, and AnnData processing pipelines. Claude Code CX Codex Cursor +1 2,400installs

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Questions about scvi-tools

How do I install scvi-tools in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill scvi-tools -a claude-code, then run npx skills add K-Dense-AI/scientific-agent-skills --skill scvi-tools -a claude-code again, and open ~/.claude/skills/scvi-tools/SKILL.md.

What does scvi-tools do?

The skill guides scvi-tools models for single-cell omics, including RNA integration, cell annotation, CITE-seq, and RNA/ATAC analysis. It also helps apply each model's data requirements.

What inputs do `SCVI` and `SysVI` require?

SCVI requires unnormalized RNA counts. SysVI requires normalized, log-transformed expression, so raw RNA counts should not be used for that model.

See also

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